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<div class="row" style="display:block"><h1 id="site-title"><span itemprop="givenName">Rui</span> <span itemprop="familyName">Wang</span> <wbr>|<wbr> <ruby>
<rb>王</rb><rp>(</rp><rt>wáng</rt><rp>)</rp></ruby>
<ruby><rb>睿</rb><rp>(</rp><rt>ruì</rt><rp>)</rp></ruby>
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<p><a href="/pages/blog.html"><strong>My Blog </strong></a></p>
<p></p>

 <p>I’m a biology college student at <a href='https://www.usts.edu.cn/'>Suzhou University of Science and Technology</a> .My research interests are bioinformatics .</p>


<p> I'm also interested in more applied problems with nice theoretical components. Here is my <a href='/files/cv.pdf'>CV</a>(last updated Oct 2020) and research statement.</p>


<p>In my spare time, I maintain a <a href='https://sourl.cn/xdtkdU'>WeChat Official Accounts</a> Run blog “Biology Every Day”, breaking down newest research and biology findings into layman terms.</p>

<p>You can contact me through email <a href='mailto:wangrui.ts@qq.com'>wangrui.ts@qq.com</a>.</p>

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	<div class="row pubtypeheader" id="pub-toggle">
  <span>Selected Publications<br /><span style="font-size:0.6em" onclick="togglePublication()"><em><a>See all publications.</a></em></span></span> 
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<div class="cv-non-selected row pubtypeheader">Conference Publications</div>
  <!-- Marking Streets to Improve Parking Density  -->
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      <cite class="paper-title">Marking Streets to Improve Parking Density</cite>
         <!-- 共同作者  --> 
        <ul class="coauthor-list">
        <li>
            <a href="http://www3.cs.stonybrook.edu/~skiena/">Steven Skiena</a></li></ul>
       <p><em>
	 
	  <!-- 期刊名字  -->  
          <abbr title="Urban Complex Systems">Urban Complex Systems</abbr>, <time>2020</time>.
      </em><p>
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    <div class="abstract">
      <p>Street parking spots for automobiles are a scarce commodity in most urban environments. The heterogeneity of car sizes makes it inefficient to rigidly define fixed-sized spots. Instead, unmarked streets in cities like New York leave placement decisions to individual drivers, who have no direct incentive to maximize street utilization.  In this paper, we explore the effectiveness of two different behavioral interventions designed to encourage better parking, namely (1) educational campaigns to encourage parkers to "kiss the bumper" and reduce the distance between themselves and their neighbors, or (2) painting appropriately-spaced markings on the street and urging drivers to "hit the line". Through analysis and simulation, we establish that the greatest densities are achieved when lines are painted to create spots roughly twice the length of average-sized cars. Kiss-the-bumper campaigns are in principle more effective than hit-the-line for equal degrees of compliance, although we believe that the visual cues of painted lines induce better parking behavior.</p>
    </div>
  </div>
	
	
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      <cite class="paper-title">Computing minimum cuts in hypergraphs</cite>
      <ul class="coauthor-list">
        <li>
            <a href="http://chekuri.cs.illinois.edu/">Chandra Chekuri</a></li></ul>
      <p><em>
          <abbr title="ACM-SIAM Symposium on Discrete Algorithms">SODA</abbr>, <time>2017</time>.
      </em><p>
	    
        <aside class="cv-non-selected note">The SODA camera ready version has a bug in the sparsification section that is fixed in the arXiv update.</aside>
        <aside class="cv-non-selected note">The journal version with additional results was serialized as <a href="#hypergraph-min-cut-journal">Minimum cuts and sparsification in hypergraphs</a> in SICOMP.</aside>
    </div>
    <div class="abstract">
      <p>We study algorithmic and structural aspects of connectivity in hypergraphs. Given a hypergraph <span class="math">H=(V,E)</span> with <span class="math">n=|V|</span>, <span class="math">m=|E|</span> and <span class="math">p=\sum_{e\in E}|e|</span> the best known algorithm to compute a global minimum cut in <span class="math">H</span> runs in time <span class="math">O(np)</span> for the uncapacitated case and in <span class="math">O(np+n^2\log n)</span> time for the capacitated case. We show the following new results.</p>
<ol>
<li>Given an uncapacitated hypergraph <span class="math">H</span> and an integer <span class="math">k</span> we describe an algorithm that runs in <span class="math">O(p)</span> time to find a subhypergraph <span class="math">H&#x27;</span> with sum of degrees <span class="math">O(kn)</span> that preserves all edge-connectivities up to <span class="math">k</span> (a <span class="math">k</span>-sparsifier). This generalizes the corresponding result of Nagamochi and Ibaraki from graphs to hypergraphs. Using this sparsification we obtain an <span class="math">O(p+\lambda n^2)</span> time algorithm for computing a global minimum cut of <span class="math">H</span> where <span class="math">\lambda</span> is the minimum cut value.</li>
<li>We generalize Matula's argument for graphs to hypergraphs and obtain a <span class="math">(2+\e)</span>-approximation to the global minimum cut in a capacitated hypergraph in <span class="math">O(\frac{1}{\e}(p+n \log n)\log n)</span> time.</li>
<li>We show that a hypercactus representation of all the global minimum cuts of a capacitated hypergraph can be computed in <span class="math">O(np+n^2\log n)</span> time and <span class="math">O(p)</span> space.
We utilize vertex ordering based ideas to obtain our results. Unlike graphs we observe that there are several different orderings for hypergraphs which yield different insights.</li>
</ol>
    </div>
  </div>
		
 <!-- 一般-期刊 -->	
<div class="cv-non-selected row pubtypeheader">Journal Publications</div>
	
	
 
  <!-- A ferroptosis-related gene signature identified as a novel prognostic biomarker for colon cancer -->
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      <cite class="paper-title">A ferroptosis-related gene signature identified as a novel prognostic biomarker for colon cancer</cite>
      <ul class="coauthor-list">
        <li>
            <a href="http://scls.usts.edu.cn/szdw1/zzjs.htm" target="_blank" >Xin Qi</a></li></ul>
      <p><em>
          Frontiers in Genetics <time>2021</time>.
      </em><p>
    </div>
    <div class="abstract">
   <li>
   Background: Colon cancer (CC) is a common gastrointestinal malignant tumor with high heterogeneity in clinical behavior and response to treatment, making individualized survival prediction challenging. Ferroptosis is a newly discovered iron-dependent cell death that plays a critical role in cancer biology. Therefore, identifying a prognostic biomarker with ferroptosis-related genes provides a new strategy to guide precise clinical decision-making in CC patients.
   </li> <li>
   Methods: Alteration in the expression profile of ferroptosis-related genes was initially screened in GSE39582 dataset involving 585 CC patients. Univariate Cox regression analysis and LASSO-penalized Cox regression analysis were combined to further identify a novel ferroptosis-related gene signature for overall survival prediction. The prognostic performance of the signature was validated in the GSE17536 dataset by Kaplan-Meier survival curve and time-dependent ROC curve analyses. Functional annotation of the signature was explored by integrating GO and KEGG enrichment analysis, GSEA analysis and ssGSEA analysis. Furthermore, an outcome risk nomogram was constructed considering both the gene signature and the clinicopathological features.
    </li> <li>
   Results: The prognostic signature biomarker composed of 9 ferroptosis-related genes accurately discriminated high-risk and low-risk patients with CC in both the training and validation datasets. The signature was tightly linked to clinicopathological features and possessed powerful predictive ability for distinct clinical subgroups. Furthermore, the risk score was confirmed to be an independent prognostic factor for CC patients by multivariate Cox regression analysis ( p value < 0.05). Functional annotation analyses showed that the prognostic signature was closely correlated with pivotal cancer hallmarks, particularly cell cycle, transcriptional regulation, and immune-related functions. Moreover, a nomogram with the signature was also built to quantify outcome risk for each patient.
    </li><li>
   Conclusion: The novel ferroptosis-related gene signature biomarker can be utilized for predicting individualized prognosis, optimizing survival risk assessment and facilitating personalized management of CC patients. 
    </li>
	  
	  </div>
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      <cite class="paper-title">LP Relaxation and Tree Packing for Minimum <span class="math">k</span>-Cut</cite>
      <ul class="coauthor-list">
        <li>
            <a href="http://chekuri.cs.illinois.edu/">Chandra Chekuri</a></li><li>
            <a href="https://kentquanrud.com/">Kent Quanrud</a></li></ul>
      <p><em>
          SIAM Journal on Discrete Mathematics <time>2020</time>.
      </em><p>
        <aside class="cv-non-selected note">An <a href="#kcut-revisited">extended abstract</a> of this work appeared in SOSA 2019.</aside>
    </div>
    <div class="abstract">
      <p>Karger used spanning tree packings [D. R. Karger, J. ACM, 47 (2000), pp. 46--76] to derive a near linear-time randomized algorithm for the global minimum cut problem as well as a bound on the number of approximate minimum cuts. This is a different approach from his well-known random contraction algorithm [D. R. Karger, Random Sampling in Graph Optimization Problems, Ph.D. thesis, Stanford University, Stanford, CA, 1995, D. R. Karger and C. Stein, J. ACM, 43 (1996), pp. 601--640]. Thorup developed a fast deterministic algorithm for the minimum <span class="math">k</span>-cut problem via greedy recursive tree packings [M. Thorup, Minimum <span class="math">k</span>-way cuts via deterministic greedy tree packing, in Proceedings of the Fortieth Annual ACM Symposium on Theory of Computing, ACM, 2008, pp. 159--166].
In this paper we revisit properties of an LP relaxation for cͅut proposed by Naor and Rabani [Tree packing and approximating <span class="math">k</span>-cuts, in Proceedings of the Twelfth Annual ACM-SIAM Symposium on Discrete Algorithms, Vol. 103, SIAM, Philadelphia, 2001, pp. 26--27], and analyzed in [C. Chekuri, S. Guha, and J. Naor, SIAM J. Discrete Math., 20 (2006), pp. 261--271]. We show that the dual of the LP yields a tree packing that, when combined with an upper bound on the integrality gap for the LP, easily and transparently extends Karger's analysis for mincut to the <span class="math">k</span>-cut problem. In addition to the simplicity of the algorithm and its analysis, this allows us to improve the running time of Thorup's algorithm by a factor of <span class="math">n</span>. We also improve the bound on the number of <span class="math">\alpha</span>-approximate <span class="math">k</span>-cuts. Second, we give a simple proof that the integrality gap of the LP is <span class="math">2(1-1/n)</span>. Third, we show that an optimum solution to the LP relaxation, for all values of <span class="math">k</span>, is fully determined by the principal sequence of partitions of the input graph. This allows us to relate the LP relaxation to the Lagrangean relaxation approach of Barahona [Oper. Res. Lett., 26 (2000), pp. 99--105] and Ravi and Sinha [European J. Oper. Res., 186 (2008), pp. 77--90]; it also shows that the idealized recursive tree packing considered by Thorup gives an optimum dual solution to the LP.</p>
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  <!-- Minimum cuts and sparsification in hypergraphs  -->
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    <div class="cv-right">
      <cite class="paper-title">Minimum cuts and sparsification in hypergraphs</cite>
      <ul class="coauthor-list">
        <li>
            <a href="http://chekuri.cs.illinois.edu/">Chandra Chekuri</a></li></ul>
      <p><em>
          SIAM Journal on Computing <time>2018</time>.
      </em><p>
        <aside class="cv-non-selected note">The paper is a combination of <a href="#hypergraph-min-cut-conf">Computing minimum cuts in hypergraphs</a> appeared in SODA 2017 and <a href="https://arxiv.org/abs/1703.03849">A note on approximate strengths of edges in a hypergraph</a>.</aside>
    </div>
    <div class="abstract">
      <p>We study algorithmic and structural aspects of connectivity in hypergraphs. Given a hypergraph <span class="math">H=(V,E)</span> with <span class="math">n = |V|</span>, <span class="math">m = |E|</span> and <span class="math">p = \sum_{e \in E} |e|</span> the fastest known algorithm to compute a global minimum cut in <span class="math">H</span> runs in <span class="math">O(np)</span> time for the uncapacitated case, and in <span class="math">O(np + n^2 \log n)</span> time for the capacitated case. We show the following new results.</p>
<ul>
<li>Given an uncapacitated hypergraph <span class="math">H</span> and an integer <span class="math">k</span> we
   describe an algorithm that runs in <span class="math">O(p)</span> time to find a (trimmed)
   subhypergraph <span class="math">H&#x27;</span> with sum of degrees <span class="math">O(kn)</span> that preserves all
   edge-connectivities up to <span class="math">k</span> (a <span class="math">k</span>-sparse certificate). This
   generalizes the corresponding result of Nagamochi and Ibaraki from
   graphs to hypergraphs. Using this sparsification we obtain an <span class="math">O(p + \lambda n^2)</span> time algorithm for computing a global minimum cut of
   <span class="math">H</span> where <span class="math">\lambda</span> is the minimum cut value.</li>
<li>We show that a hypercactus representation of <em>all</em> the
   global minimum cuts of a capacitated hypergraph can be computed in
   <span class="math">O(np + n^2 \log n)</span> time and <span class="math">O(p)</span> space matching the asymptotic
   time to find a single minimum cut.</li>
<li>We obtain a <span class="math">(2+\e)</span>-approximation to the global minimum cut
   of a capacitated hypergraph in <span class="math">O(\frac{1}{\e} (p \log n + n \log^2 n))</span>
   time, and for uncapacitated hypergraphs in <span class="math">O(p/\e)</span> time.
   We achieve this by generalizing Matula's algorithm for
   graphs to hypergraphs.</li>
<li>We describe an algorithm to compute approximate strengths of
all the edges of a hypergraph in <span class="math">O(p \log^2 n \log p)</span> time. This
gives a near linear time algorithm for finding a <span class="math">(1+\e)</span>-cut
sparsifier based on the work of Kogan and Krauthgamer. As a
byproduct we obtain faster algorithms for various cut and flow
problems in hypergraphs of small rank.</li>
</ul>
<p>Our results build upon properties of vertex orderings that were inspired by the maximum adjacency ordering for graphs due to Nagamochi and Ibaraki.  Unlike graphs we observe that there are several orderings for hypergraphs and these yield different insights.</p>
    </div>
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<!-- 手稿-未发表  -->
	
  <!-- An algorithm for the metric multiple depots capacitated vehicle routing problem with restocking and capacity two  -->
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      <cite class="paper-title">An algorithm for the metric multiple depots capacitated vehicle routing problem with restocking and capacity two</cite>
      <ul class="coauthor-list">
        <li>
            Yichen Yang</li><li>
            <a href="http://qianzhang.me/">Qian Zhang</a></li></ul>
      <p><em>
        2019, Submitted.
      </em><p>
    </div>
    <div class="abstract">
      <p>The capacitated vehicle routing problem (CVRP) is one of the most well known NP-hard combinatorial optimization problems. Single depot CVRP with a general metric is NP-hard even for fixed capacity 3, while polynomial time solvable for fixed capacity 2. We consider the variant of CVRP where restocking is available. We show that if there is a constant number of depots, then the problem can be solved in polynomial time when capacity is <span class="math">2</span>.</p>
    </div>
  </div>
<div class="cv-non-selected row pubtypeheader">Thesis</div>
  <!-- Cuts and Connectivity in Graphs and Hypergraphs  -->
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    <div class="cv-right">
      <cite class="paper-title">Cuts and Connectivity in Graphs and Hypergraphs</cite>
      <p><em>
        <time>2018</time>.
      </em><p>
        <aside class="cv-non-selected note">Nominated for the <a href="https://awards.acm.org/doctoral-dissertation">ACM Doctoral Dissertation Award</a> by Department of Computer Science at UIUC.</aside>
    </div>
    <div class="abstract">
      <p>In this thesis, we consider cut and connectivity problems on graphs, digraphs, hypergraphs and hedgegraphs. The main results are the following:</p>
<ul>
<li>We introduce a faster algorithm for finding the reduced graph in element-connectivity computations. We also show its application to node separation.</li>
<li>We present several results on hypergraph cuts, including (a) a near linear time algorithm for finding a (2 + ε)-approximate min-cut, (b) an algorithm to find a representation of all min-cuts in the same time as finding a single min-cut, (c) a sparse subgraph that preserves connectivity for hypergraphs and (d) a near linear-time hypergraph cut sparsifier.</li>
<li>We design the first randomized polynomial time algorithm for the hypergraph <span class="math">k</span>-cut problem whose complexity has been open for over 20 years. The algorithm generalizes to hedgegraphs with constant span.</li>
<li>We address the complexity gap between global vs. fixed-terminal cuts problems in digraphs by presenting a <span class="math">2-\frac{1}{448}</span> approximation algorithm for the global bicut problem.</li>
</ul>
        <aside class="dedication">Co-advised by <a href="http://karthik.ise.illinois.edu/">Karthik Chandrasekaran</a> and <a href="http://chekuri.cs.illinois.edu/">Chandra Chekuri</a>.</aside>
    </div>
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